ISSRs (Inter Simple Sequence Repeats) were employed to compare the genetic structure of Chthamalus stellatus and Tesseropora atlantica in the Azores. The two barnacles differ as regards life cycle: the former conducting pelagic life for about 22 days, the latter for only 24 h. Thirty individuals of each species were analysed from four locations of three Azorean islands. Five ISSR primers produced, respectively, 117 and 79 polymorphic bands in C. stellatus and T. atlantica. Estimates of among-samples genetic diversity suggested extensive connectivity in the former species and isolation in the latter. AMOVA further supported these results by attributing 2% of genetic variance to the among-islands component of C. stellatus and 30% to T. atlantica. Results are consistent with expectations based on species life history and corroborate the importance of pelagic stages in determining the degree of genetic structuring in benthic marine invertebrates.